Patel, A;
Hayward, JD;
Tailor, V;
Nyanhete, R;
Ahlfors, H;
Gabriel, C;
Jannini, TB;
... Sowden, JC; + view all
(2019)
The Oculome panel test: next-generation sequencing to diagnose a diverse range of genetic developmental eye disorders.
Ophthalmology
, 126
(6)
pp. 888-907.
10.1016/j.ophtha.2018.12.050.
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Abstract
PURPOSE: To develop a comprehensive next-generation sequencing panel assay which screens genes known to cause developmental eye disorders and inherited eye disease (Oculome test) and to evaluate its diagnostic yield in a paediatric cohort with malformations of the globe, anterior segment anomalies and/or childhood glaucoma. DESIGN: Evaluation of diagnostic test. PARTICIPANTS: 277 children age 0-16 years diagnosed with nonsyndromic or syndromic developmental eye defects without a genetic diagnosis. METHODS: We developed a new Oculome panel using a custom-designed Agilent SureSelect QXT target capture method to capture and perform parallel high through put sequencing analysis of 429 genes associated with eye disorders. We confirmed suspected pathogenic variants by bidirectional Sanger sequencing. MAIN OUTCOME MEASURES: We collated clinical details and the oculome molecular genetic results. RESULTS: The Oculome design covers 429 known eye disease genes; these are subdivided into 5 overlapping virtual sub-panels for anterior segment developmental anomalies and glaucoma (ASDA; 59 genes), microphthalmia-anophthalmia-coloboma (MAC; 86 genes), congenital cataracts and lens-associated conditions (CAT; 70 genes), retinal dystrophies (RET; 235 genes), and albinism (15 genes), and as well as additional genes implicated in optic atrophy and complex strabismus (10 genes). Panel development and testing included analysing n = 277 clinical samples and 3 positive control samples using Illumina sequencing platforms; >30 X read-depth was achieved for 99.5% of the targeted 1.77 Mb region. Bioinformatics analysis performed using a pipeline based on Freebayes and ExomeDepth to identify coding sequence and copy number variants respectively, resulted in a definitive diagnosis in 68 / 277 cases with variability in diagnostic yield between phenotypic sub-groups; MAC: 8.2% (8 of 98 cases solved), ASDA: 24.8% (28 of 113 cases solved), other / syndromic 37.5% (3 of 8 cases solved); RET: 42.8% (21 of 49 cases solved); CAT: 88.9% (8 of 9 cases solved). CONCLUSION: The Oculome test diagnoses a comprehensive range of genetic conditions affecting the development of the eye, potentially replacing protracted and costly multidisciplinary assessments and allowing for faster targeted management. The Oculome enabled the molecular diagnosis of a significant number of cases in our sample cohort of varied ocular birth defects.
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